For D2 eligibility, it depends upon if he was actually enrolled in school during that period of time. D2 does a count of semesters of enrollment (or quarters as the case may be) to determine the eligibility limit.
From the NCAA:
Each Division II student-athlete has 10 semesters or 15 quarters of full-time collegiate enrollment in order to participate as a student-athlete. Within these 10 semesters or 15 quarters, a student-athlete has four years of athletics eligibility (seasons of competition) in which he or she can participate against outside competition.
If he was enrolled in school for the entire 2 years, then he has 6 semesters of eligibility left. Since football is a single semester sport (unlike basketball, wrestling, etc.) you could play with your enrollment to get 4 years of football by not being enrolled in school for one of the spring semesters. But then, by rule, you couldn't do the weight program, spring practice, or any other team activities, etc.
D1 is different and it is a running clock once you enroll in school. You have 5 years to complete 4 years of competition with the clock starting once you enroll in school. That's a very simplified version but is essentially the way it works (with some exceptions - age because of delayed enrollment, military service, religious missions, medical hardship, etc.).